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Detailed information for vg0401725165:

Variant ID: vg0401725165 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1725165
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGCGAGAACTGATCAGCTATCGTACGCTTGCGTGAGCAACAACAGTTTGTGTGTTCATAGATCTACTGGCTACCATTGCAAGTGCTCTTTGGGCTACG[G/A]
AGGAAATGCCTATATCGAAGATGGCTGTGAGGGTATGCTGTCTCTGATAAGCTTGATCGCTATCGTATTTACTATCTGACTGTTTTAAGGTACACCAAAT

Reverse complement sequence

ATTTGGTGTACCTTAAAACAGTCAGATAGTAAATACGATAGCGATCAAGCTTATCAGAGACAGCATACCCTCACAGCCATCTTCGATATAGGCATTTCCT[C/T]
CGTAGCCCAAAGAGCACTTGCAATGGTAGCCAGTAGATCTATGAACACACAAACTGTTGTTGCTCACGCAAGCGTACGATAGCTGATCAGTTCTCGCTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.90%	5.50%	0.80%	33.73%	NA
All Indica	2759	52.80%	4.60%	0.91%	41.65%	NA
All Japonica	1512	75.20%	0.30%	0.73%	23.81%	NA
Aus	269	43.90%	46.10%	0.37%	9.67%	NA
Indica I	595	13.40%	10.80%	1.01%	74.79%	NA
Indica II	465	77.40%	1.50%	0.65%	20.43%	NA
Indica III	913	69.10%	1.50%	0.66%	28.70%	NA
Indica Intermediate	786	49.10%	5.50%	1.27%	44.15%	NA
Temperate Japonica	767	74.20%	0.00%	1.17%	24.64%	NA
Tropical Japonica	504	76.60%	0.40%	0.40%	22.62%	NA
Japonica Intermediate	241	75.50%	0.80%	0.00%	23.65%	NA
VI/Aromatic	96	60.40%	4.20%	1.04%	34.38%	NA
Intermediate	90	68.90%	2.20%	0.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401725165	G -> DEL	LOC_Os04g03830.1	N	frameshift_variant	Average:30.311; most accessible tissue: Callus, score: 62.575	N	N	N	N
vg0401725165	G -> A	LOC_Os04g03830.1	missense_variant ; p.Gly197Glu; MODERATE	nonsynonymous_codon ; G197E	Average:30.311; most accessible tissue: Callus, score: 62.575	benign	-0.208	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401725165	NA	7.57E-07	mr1038	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	4.01E-06	mr1048	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	7.19E-06	mr1073	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	2.87E-07	mr1126	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	3.93E-08	mr1348	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	4.81E-06	mr1353	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	9.92E-06	mr1372	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	4.30E-06	mr1382	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	1.36E-07	mr1389	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	5.68E-09	mr1545	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	4.20E-06	mr1774	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	3.58E-07	mr1931	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	1.98E-06	mr1038_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0401725165	NA	8.48E-07	mr1389_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251